Captain America - Ice
Daredevil - Underboss
X-Men - The Draco (I know Austen is universally hated but I thought The Draco was his best X-Men story, at least better than crap like Holy War or Dominant Species, if that means anything)
Mark Waid's run on Cap was pretty underrated as well.
The Thing's solo series from the `80's. I thought Ben as a wrestler was an entertaining concept towards the end of the series...
The Defenders #41-91, or as I call them -- the anti-Gerber stories.
Bob Harras' Avengers.
Damn...I had a list of answers, but am completely blanking on the rest of them.
Peter David's 1990s first run on X-Factor, before X-Factor Investigations.
The 90's Foolkiller maxi-series written by Steve Gerber is one of the best comics I've ever read and I'm amazed Marvel has never collected in in trade form.
Another great one was the English translation of Spider-Man the Manga, not the Mangaverse version but the actual Japanese comic version of Spider-Man that Marvel did an English adaption of back in the late 90's I'm always amazed that Marvel has never tried to do trades on this run as I think both Spider-Man fans and Manga fans would really enjoy it.
Dan Jurgens' run on Thor. JMS' run gets more publicity but is considerably inferior (and I liked the JMS run) to Jurgens'.
ROM never gets enough love these days. That series was great from issue 1 all the way to the end of the Dire Wraiths War.